Currently, there is considerable interest in the development of inhibitors of Tdp1 enzyme, which is considered a promising target enzyme for the development of drugs for treating oncological and neurodegenerative diseases [1].
Tdp1 is a phosphodiesterase, a class of enzymes which breaks phosphodiester bonds [2]. Tdp1 plays an important role in repairing the DNA damage induced by topoisomerase 1 (Top1) inhibitor camptothecin and other antitumor drugs. The normal enzymatic cycle of Top1 includes a reversible transesterification reaction. Tyrosine-723 residue of the enzyme's active center forms a transient covalent complex with 3′-phosphate of the DNA backbone, creating a single strand break, which allows the «broken» strand to rotate around the intact one, relaxing the local tension in the DNA helix. Then the integrity of the DNA is restored by a reverse reaction (ligation). In normal conditions the speed of ligation reaction is far greater than the breaking reaction, but in some cases the transient complexes remain stable. In particular, Top1 inhibitors, such as camptothecin and its clinically used derivatives, considerably slow down the ligation reaction [3]. The inability to restore the DNA structure results in single-strand breaks, which can subsequently turn into more toxic double-strand breaks. In addition to inhibitors, certain damage of DNA near the Top1 attachment site can also block the ligation reaction.
Tdp1 breaks the 3′-diester bond between the tyrosine residue and the 3′-end of the DNA, while also removing other types of damage from the 3′-end of the DNA [4,5]. At the same time, a phosphate remains at the 3′-end of the DNA, while a hydroxyl residue remains at the 5′-end. Such structure is a substrate for polynucleotide kinase 3′-phosphatase (PNKR) enzyme, which restores the 3′-OH, 5′-phosphate configuration, traditional for base excision repair (BER) [6]. As a result, Tdp1 reduces the efficacy of Top1 inhibitors, which are otherwise rather effective as anticancer drugs (see reviews [7, 8]). It is theorized that Tdp1 is responsible for the drug resistance of several types of cancer [3, 9]. This theory is confirmed by several studies: mice with Tdp1 knockout and human cell lines with SCAN1 mutations are hypersensitive to camptothecin [10-13]. On the other hand, camptothecin and etoposide induce less DNA damage in cells with increased level of Tdp1 expression [14, 15]. Thus, combining drugs acting on Top1 and Tdp1 can considerably increase the efficacy of chemotherapy.
It is also known that inhibiting Tdp1 activity makes tumor cells hypersensitive to anticancer drugs temozolomide (purine methylation) [16], methyl methanesulfonate (generation of apurinic/apyrimidinic site sites), bleomycin (single-strand/double-strand breaks with 3′-phosphoglycolates), hydrogen peroxide and ionizing radiation (strand breaks and other types of damage) [17]. This demonstrates that Tdp1 participates in different pathways of DNA repair.
Thus, Tdp1 inhibitors may be therapeutically useful for selectively enhancing the activity of antitumor drugs.
There are relatively few Tdp1 inhibitors described in the literature [18-28]. A major drawback of the known compounds is their relatively low inhibition potency towards Tdp1 (IC50 ranges from 0.2 to 100 μM).
The compound, most similar to the present invention (a prototype), is furamidine, a heterocyclic diamidine [20] of formula II:

A drawback of this compound is its low inhibition potency towards Tdp1 (IC50 for single-strand DNA is about 100 μM).